However, I do not see how much this would affect the (AFAIK) main
complaint about multi-window GIMP: that having several windows with
several possibilities of what is focused requires many extraneous
mouse clicks and/or keypresses.

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the introduction of a single window mode is in no way related to that.

When the windows are merged into one, STILL only one of subwindows has
a focus? So how does this improves the current nightmares (e.g.,
keyboard shortcuts not working - especially when most needed ;-)?

that is a serious bug.
in what version(s) of GIMP does this happen?
--ps
founder + principal interaction architect
man + machine interface works
http://mmiworks.net/blog : on interaction architecture